export Assets and import in Relion

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rddey80
export Assets and import in Relion

Dear Members,

I exported an asset in relion format from cisTEM and it created a stack file and a star file. Can someone tell step by step how I can use these two files to run 2D classification in Relion? I tried, but it did not work for me. What I did in Relion, is as follows:

1. Imported motion corrected mrc files, that created micrographs.star file

2. used particle extraction as attached screenshot

where to use the stack file?

Thanks for your time,

raj

timgrant
Hi Raj,

Hi Raj,

You should be able to straight to the 2D classification job line in Relion, select the star file that you exported from cisTEM, setup your parameters and run.

Cheers!

Tim

rddey80
export Assets and import in Relion

Hi Tim,

Mant thanks for your reply. I tried and got an error as follows:

Error:

cannot read file*-stack it does not exist

File: /usr/local/src/relion/src/image.h line: 157

Any idea?

Thanks,

Raj

timgrant
Did you move the stack after

Did you move the stack after you exported it?

Cheers,

Tim

rddey80
Hi Tim,

Hi Tim,

No, I did not move. Both star and stack files are located at the same place where cisTEM exported. Please see below:

[rdey@phoebe cistem]$ pwd
/ddn/TarkD/prex2/cistem
[rdey@phoebe cistem]$ ls

micrographs-neg  micrographs-pp  prex2-225k-stack  prex2-225k-star.star  prex2-neg  prex2-pp
[rdey@phoebe cistem]$ cd ../relion/

[rdey@phoebe relion]$  

I ran Relion 2D Classification here browsing the *.star file in the input gui and got the following error

ERROR:
Cannot read file prex2-225k-stack It does not exist
File: /usr/local/src/relion/src/image.h line: 157

Thanks,

Raj

timgrant
Hi Rak,

Hi Raj,

It is strange it does not have an extension, it should have the .mrcs extension.  Can you try to export it again with the filename prex2-225k-stack.mrcs

Thanks,

Tim

rddey80
Hi Tim,

Hi Tim,

Thanks. It is now running.

Best regards,

Raj

moritz
similar issue with stack file

Hello,

I tried something similar to Raj (exporting particles for use in relion) and got the stack and star files.  Relion couldn't open the stack, so I tried exporting again, adding the .mrcs extension to the stack file.  This made the cisTEM GUI crash with the following error:

(cisTEM:9636): Gtk-CRITICAL **: 15:23:22.330: IA__gtk_tree_row_reference_new_proxy: assertion 'path->depth > 0' failed
Error: mode 32528 MRC files not currently supported

I also had to move my whole project to a new directory before I tried the second export with the .mrcs extension, so I'm not sure if that's what the first line of the error is referring to, but also wondered about the "MRC files not currently supported" error.

thanks for your help,

Michelle

timgrant
Hi Michelle,

Hi Michelle,

That error is also given when the file does not exist (confusing I know). Which may be what is happening in your case.

Tim

rddey80
using earlier 2D class average to re-pick particles

Hi Tim,

I have a good ab-intio 3D map generated from a refinement package, which is created from a number of selected 2D class averages (all done in cisTEM). Is it possible to use the 3D ab-initio map or the 2D class avegares to re-pick particles in cisTEM? If not, can I switch to relion to do the same? In that case, could you please guide how to do that? I mean, which file to export? 

Thanks for your time and help,

Raj

timgrant
Hi Raj,

Hi Raj,

cisTEM does not use references to do the picking, so you can't do this.  

Is there a reason why you are keen to do this? Did the picking not work well?

Tim

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